Plant Editosome Database
a curated database of RNA editosome in plants

CLB19 - Plant Editosome Database - BIG Data Center
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Summary

Editing Factor: CLB19
Synonym: CHLOROPLAST BIOGENESIS 19; PDE247; PIGMENT DEFECTIVE 247
Description: Encoding a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts
Protein Family: PPR
Subclass: E+
Construct Structure: PLS-E-E+
Gene ID & Species: AT1G05750 (Arabidopsis thaliana)
Edited Gene(s): rpoA    clpP
Editing Type(s): C-to-U (36)
Publication(s): [1] The Analysis of the Editing Defects in the Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins., Plants (Basel, Switzerland), 2020. [PMID=32098170]
[2] Multiple PPR protein interactions are involved in the RNA editing system in mitochondria and plastids., Proceedings of the National Academy of Sciences of the United States of America, 2017. [PMID=28761003]
[3] Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein., The New phytologist, 2015. [PMID=25980341]
[4] Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis., The Plant cell, 2015. [PMID=25649437]
[5] CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts., The Plant journal : for cell and molecular biology, 2008. [PMID=18657233]

Editing Details

Species Gene ID Organelle Edited Gene Position Region Editing Type Codon Amino Acid Molecular Effect Experiment Details
Arabidopsis thaliana AT1G05750 Chloroplast
Plastid		 clpP 559 CDS C-to-U CAU=>UAU
CAC=>UAC
NA=>NA		 H=>Y
NA=>NA		 Recoding
NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
NAclb19-1T-DNA InsertionT-DNA is inserted at codon 230NAPale-yellow cotyledons and seedling leaves when grown under standard light conditions and dies shortly afterwardsSeedlingNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent18657233
SALK_123752clb19-3T-DNA InsertionNANASeedlings with a pale-yellow phenotypeSeedlingNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent18657233
Col-0Col-0ControlControlControlNormalSeedlingNAPoisoned Primer Extension (PPE) AssayNAHighNone18657233
NATCComplementationNANANASeedlingNAPoisoned Primer Extension (PPE) AssayNAHighRestored18657233
NACLB19-HisOverexpressionNANANANANAGel electrophoretic mobility shift assaysNANANA25980341
NACLB19△E-HisOverexpressionNANANANANAGel electrophoretic mobility shift assaysNANANA25980341
Col-0WTControlControlControlNANANARNA-seq71.85%HighNone32098170
Col-0WTControlControlControlNormalLeafNART-PCR and calculated with the DNADynamo software (BlueTract67.00%HighNone28761003
Col-0DYW2-GFP-OE1Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independenNASlow growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract7.00%PoorDecreased28761003
Col-0DYW2-GFP-OE2Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independenNASlow growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract1.00%PoorDecreased28761003
Arabidopsis thaliana AT1G05750 Plastid clpP NA NA C-to-U NA=>NA NA=>NA NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
Col-0WTControlControlControlNANA3 weeksPoisoned primer extension (PPE) analysis89.33%HighNone25649437
SALK_104250CLB19wtComplementedPlants transformed with wild-type CLB19 driven by the same promoter as used to drive expression of the variants.NANANA3 weeksPoisoned primer extension (PPE) analysis89.80%HighRestored25649437
SALK_104250S2[TD]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis89.00%HighSimilar25649437
SALK_104250S2[TN]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis87.17%HighSimilar25649437
SALK_104250S2[SD]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis51.67%MediumDecreased25649437
SALK_104250S3[TT]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis40.17%MediumDecreased25649437
SALK_104250S3[TD]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis20.67%LowDecreased25649437
SALK_104250c19A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis0.00%UneditedAbsent25649437
Arabidopsis thaliana AT1G05750 Chloroplast
Plastid		 rpoA 200 CDS C-to-U UCU=>UUU
NA=>NA		 S=>F
NA=>NA		 Recoding
NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
NAclb19-1T-DNA InsertionT-DNA is inserted at codon 230NAPale-yellow cotyledons and seedling leaves when grown under standard light conditions and dies shortly afterwardsSeedlingNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent18657233
SALK_123752clb19-3T-DNA InsertionNANASeedlings with a pale-yellow phenotypeSeedlingNAPoisoned Primer Extension (PPE) Assay0.00%UneditedAbsent18657233
Col-0Col-0ControlControlControlNormalSeedlingNAPoisoned Primer Extension (PPE) AssayNAHighNone18657233
NATCComplementationNANANASeedlingNAPoisoned Primer Extension (PPE) AssayNAHighRestored18657233
NACLB19-HisOverexpressionNANANANANAGel electrophoretic mobility shift assaysNANANA25980341
NACLB19△E-HisOverexpressionNANANANANAGel electrophoretic mobility shift assaysNANANA25980341
Col-0WTControlControlControlNANANARNA-seq75.94%HighNone32098170
Col-0WTControlControlControlNormalLeafNART-PCR and calculated with the DNADynamo software (BlueTract74.00%HighNone28761003
Col-0DYW2-GFP-OE1Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independenNASlow growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract4.00%PoorDecreased28761003
Col-0DYW2-GFP-OE2Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 geneCol-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independenNASlow growthLeafNART-PCR and calculated with the DNADynamo software (BlueTract5.00%PoorDecreased28761003
Arabidopsis thaliana AT1G05750 Plastid rpoA NA NA C-to-U NA=>NA NA=>NA NA
Experiment Details
Genotype (Ecotype) Allele Treatment Treatment Detail Mutant Type Phenotype Tissue Development Stage Detection Method Editing Frequency Editing Extent Mutant Effect PMID
Col-0WTControlControlControlNANA3 weeksPoisoned primer extension (PPE) analysis75.67%HighNone25649437
SALK_104250CLB19wtComplementedPlants transformed with wild-type CLB19 driven by the same promoter as used to drive expression of the variants.NANANA3 weeksPoisoned primer extension (PPE) analysis78.80%HighRestored25649437
SALK_104250S2[TD]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis69.17%HighSimilar25649437
SALK_104250S2[TN]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis72.67%HighSimilar25649437
SALK_104250S2[SD]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis49.80%MediumDecreased25649437
SALK_104250S3[TT]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis73.17%HighSimilar25649437
SALK_104250S3[TD]A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis78.00%HighSimilar25649437
SALK_104250c19A T-DNA insertionA T-DNA insertion (SALK_104250) in At1g05750NANANA3 weeksPoisoned primer extension (PPE) analysis0.33%PoorDecreased25649437
Last update: Jul 2021 (version 1.0)